Skip to content

Latest commit

 

History

History
194 lines (125 loc) · 5.95 KB

install_pysteps.rst

File metadata and controls

194 lines (125 loc) · 5.95 KB
Raw

Installing pysteps

Dependencies

The pysteps package needs the following dependencies

Additionally, the following packages can be installed for better computational efficiency:

  • dask and toolz (for code parallelization)
  • pyfftw (for faster FFT computation)

Other optional dependencies include:

Important: If you only want to use pysteps, you can continue reading below. But, if you want to contribute to pysteps or edit the package, you need to install pysteps in development mode: :ref:`Contributing to pysteps <contributor_guidelines>`.

Anaconda install (recommended)

Conda is an open-source package management system and environment management system that runs on Windows, macOS, and Linux. Conda quickly installs, runs, and updates packages and their dependencies. It also allows you to easily create, save, load, or switch between different environments on your local computer.

Since version 1.0, pySTEPS is available in conda-forge, a community-driven package repository for anaconda.

There are two installation alternatives using anaconda: install pySTEPS in a pre-existing environment or install it new environment.

New environment

In a terminal, to create a new conda environment and install pySTEPS, run:

$ conda create -n pysteps
$ source activate pysteps

This will create and activate the new python environment. The next step is to add the conda-forge channel where the pySTEPS package is located:

$ conda config --env --prepend channels conda-forge

Let's set this channel as the priority one:

$ conda config --env --set channel_priority strict

The latter step is not strictly necessary but is recommended since the conda-forge and the default Anaconda channels are not 100% compatible.

Finally, to install pySTEPS and all its dependencies run:

$ conda install pysteps

Install from source

The recommended way to install pysteps from the source is using pip to adhere to the [PEP517 standards](https://www.python.org/dev/peps/pep-0517/). Using pip instead of setup.py guarantees that all the package dependencies are properly handled during the installation process.

OSX users: gcc compiler

pySTEPS uses Cython extensions that need to be compiled with multi-threading support enabled. The default Apple Clang compiler does not support OpenMP. Hence, using the default compiler would have disabled multi-threading and may raise the following error during the installation:

clang: error: unsupported option '-fopenmp'
error: command 'gcc' failed with exit status 1

To solve this issue, obtain the latest gcc version with Homebrew that has multi-threading enabled:

brew install gcc

To make sure that the installer uses the homebrew's gcc, export the following environmental variables in the terminal (supposing that gcc version 8 was installed):

export CC=gcc-8
export CXX=g++-8

First, check that the homebrew's gcc is detected:

which gcc-8

This should point to the homebrew's gcc installation.

Under certain circumstances, Homebrew does not add the symbolic links for the gcc executables under /usr/local/bin. If that is the case, specify the CC and CCX variables using the full path to the homebrew installation. For example:

export CC=/usr/local/Cellar/gcc/8.3.0/bin/gcc-8
export CXX=/usr/local/Cellar/gcc/8.3.0/bin/g++-8

Then, you can continue with the normal installation procedure described next.

Installation using pip

The latest pysteps version in the repository can be installed using pip by simply running in a terminal:

pip install git+https://github.com/pySTEPS/pysteps

Or, from a local copy of the repo:

git clone https://github.com/pySTEPS/pysteps
cd pysteps
pip install .

The above commands install the latest version of the master branch, which is continuously under development.

Setting up the user-defined configuration file

The pysteps package allows the users to customize the default settings and configuration. The configuration parameters used by default are loaded from a user-defined JSON file and then stored in the pysteps.rcparams, a dictionary-like object that can be accessed as attributes or as items.

.. toctree::
    :maxdepth: 1

    Set-up the user-defined configuration file <set_pystepsrc>
    Example pystepsrc file <pystepsrc_example>

Final test: import pysteps in Python

Activate the pysteps environment:

conda activate pysteps

Launch Python and import pysteps:

python
>>> import pysteps

Important: The Python interpreter must be launched outside of the pysteps directory. Otherwise, it confuses the name of the directory with the package name. See :ref:`Issue 40 <https://github.com/pySTEPS/pysteps/issues/40>`.